[Chimera-users] reg. ribbon reprsentation

[Elaine Meng]

>>
>> Greetings. I have already posted a similar question on the forum  
>> previously and hence i am writing to your email. My problem is when  
>> i open a protein pdb, i get wonderful ribbon representation when i  
>> opt for it. But when i give a protein pdb with only a CA atoms/ 
>> CA,C,N atoms, i dnt get the ribbon representation. I understand  
>> that ribbon is constructed by considering CA,C,N,O and OXT atoms.  
>> What i did was that i simply removed O and OXT atoms by going  
>> through Tools--> Depiction --> Ribbon style Editor. It may be a  
>> wrong idea to do that. But i would appreciate if you could write me  
>> some way to draw the ribbon for protein having only CA or CA,C,N  
>> atoms IF POSSIBLE.
>>
>> Regards,
>> Bala
>>

Hi Bala,
If you have  N-CA-C atoms, it actually works pretty well if you open  
Ribbon Style Editor, go to the "Residue Class" tab, choose "amino  
acid" but then change the "Orientation atom" to C instead of O, and  
Apply.  (You still need to show ribbon if you didn't already do  
that.)  You can save and name the new residue class for re-use in some  
later Chimera session if you want.  The resulting ribbon looks the  
same to me as the standard ribbon made from N,CA,C,O (I tested this by  
writing a PDB of only the N,CA,C atoms from a complete structure,  
reading it back in, and experimenting with Ribbon Style Editor).
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbonstyle.html#class

If you have CA atoms only, then there is no way to figure out the  
plane of the ribbon - it does not work to set both the "Guide atom"  
and "Orientation atom" to CA.  Unfortunately this prevents you from  
displaying "licorice" ribbons even though they don't use an  
orientation plane.  My only solution in this case is to use some  
program to build the additional atoms from the CA trace, for example  
this web server:

http://www.ebi.ac.uk/Tools/maxsprout/index.html

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html